Variant report

Variant	rs12443171
Chromosome Location	chr15:50437815-50437816
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50408827..50409344-chr15:50437706..50438255,2	K562	blood:
2	chr15:49663197..49663716-chr15:50437294..50437821,2	K562	blood:
3	chr15:49898696..49899496-chr15:50437276..50438044,3	MCF-7	breast:
4	chr15:50437465..50438280-chr15:50607926..50608913,5	MCF-7	breast:
5	chr15:50437707..50440587-chr15:50443318..50445441,2	MCF-7	breast:
6	chr15:50433897..50436991-chr15:50437166..50439975,3	MCF-7	breast:
7	chr15:50436327..50442259-chr15:50645496..50648593,7	MCF-7	breast:
8	chr15:50343838..50344709-chr15:50437300..50438173,3	MCF-7	breast:
9	chr15:50436281..50440300-chr15:50607004..50610746,4	MCF-7	breast:
10	chr15:50435789..50439310-chr15:50472898..50476135,3	MCF-7	breast:
11	chr15:50428036..50430534-chr15:50437642..50439457,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000104064	Chromatin interaction
ENSG00000140284	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000104043	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10152738	0.81[ASN][1000 genomes]
rs10519262	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070750	0.81[ASN][1000 genomes]
rs11070751	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070752	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs11070753	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11631433	0.80[ASN][1000 genomes]
rs11632133	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634271	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11637647	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11638799	0.82[YRI][hapmap]
rs12439182	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442998	0.81[ASN][1000 genomes]
rs12591791	0.81[ASN][1000 genomes]
rs12901981	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12902997	0.81[ASN][1000 genomes]
rs12904370	0.82[CEU][hapmap]
rs12915042	0.82[YRI][hapmap]
rs12915230	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915287	0.91[JPT][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]
rs12915987	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2414025	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28403229	0.81[ASN][1000 genomes]
rs34146758	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4774556	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4775865	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5025069	0.81[ASN][1000 genomes]
rs5026421	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67251119	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7165446	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7171888	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7402755	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8023371	0.82[ASN][1000 genomes]
rs8037555	0.81[ASN][1000 genomes]
rs8041124	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs933854	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv904208	chr15:50428495-50457858	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12443171	ATP8B4	cis	multi-tissue	Pritchard

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50430600-50442600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:50434400-50438800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr15:50434600-50439400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:50436000-50438200	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr15:50436800-50438000	Enhancers	NHDF-Ad	bronchial
6	chr15:50436800-50438200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:50436800-50439200	Enhancers	Hela-S3	cervix
8	chr15:50437000-50438000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:50437000-50438000	Enhancers	Colon Smooth Muscle	Colon
10	chr15:50437000-50438000	Enhancers	HSMM	muscle
11	chr15:50437000-50438000	Enhancers	HSMMtube	muscle
12	chr15:50437000-50438000	Enhancers	Osteobl	bone
13	chr15:50437000-50438800	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr15:50437000-50439400	Enhancers	A549	lung
15	chr15:50437200-50438000	Enhancers	Adipose Nuclei	Adipose
16	chr15:50437200-50438200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:50437200-50438200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:50437400-50438000	Enhancers	Brain Hippocampus Middle	brain
19	chr15:50437400-50439400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:50437600-50438000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:50437600-50438000	Enhancers	Muscle Satellite Cultured Cells	--
22	chr15:50437600-50438000	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr15:50437600-50438200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr15:50437600-50439000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:50437600-50439400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:50437800-50438000	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr15:50437800-50438800	Enhancers	Liver	Liver
28	chr15:50437800-50441200	Weak transcription	HMEC	breast
29	chr15:50437800-50441200	Weak transcription	NHEK	skin

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